{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,30]],"date-time":"2026-08-30T05:32:05Z","timestamp":1788067925581,"version":"build-2784847793"},"reference-count":95,"publisher":"Public Library of Science (PLoS)","issue":"3","license":[{"start":{"date-parts":[[2023,3,30]],"date-time":"2023-03-30T00:00:00Z","timestamp":1680134400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001691","name":"Japan Society for the Promotion of Science","doi-asserted-by":"publisher","award":["17K20145"],"award-info":[{"award-number":["17K20145"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001381","name":"National Research Foundation Singapore","doi-asserted-by":"publisher","award":["NRF2011NRF-NRFF001-042"],"award-info":[{"award-number":["NRF2011NRF-NRFF001-042"]}],"id":[{"id":"10.13039\/501100001381","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007449","name":"Takeda Science Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100007449","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"abstract":"<jats:p>Small regulatory RNAs (sRNAs) are involved in antiviral defense and gene regulation. Although roles of RNA-dependent RNA Polymerases (RdRPs) in sRNA biology are extensively studied in nematodes, plants and fungi, understanding of RdRP homologs in other animals is still lacking. Here, we study sRNAs in the ISE6 cell line, which is derived from the black-legged tick, an important vector of human and animal pathogens. We find abundant classes of ~22nt sRNAs that require specific combinations of RdRPs and sRNA effector proteins (Argonautes or AGOs). RdRP1-dependent sRNAs possess 5\u2019-monophosphates and are mainly derived from RNA polymerase III-transcribed genes and repetitive elements. Knockdown of some RdRP homologs misregulates genes including RNAi-related genes and the regulator of immune response Dsor1. Sensor assays demonstrate that Dsor1 is downregulated by RdRP1 through the 3\u2019UTR that contains a target site of RdRP1-dependent repeat-derived sRNAs. Consistent with viral gene repression by the RNAi mechanism using virus-derived small interfering RNAs, viral transcripts are upregulated by AGO knockdown. On the other hand, RdRP1 knockdown unexpectedly results in downregulation of viral transcripts. This effect is dependent on Dsor1, suggesting that antiviral immunity is enhanced by RdRP1 knockdown through Dsor1 upregulation. We propose that tick sRNA pathways control multiple aspects of immune response via RNAi and regulation of signaling pathways.<\/jats:p>","DOI":"10.1371\/journal.pone.0281195","type":"journal-article","created":{"date-parts":[[2023,3,30]],"date-time":"2023-03-30T13:54:00Z","timestamp":1680184440000},"page":"e0281195","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":8,"title":["A novel eukaryotic RdRP-dependent small RNA pathway represses antiviral immunity by controlling an ERK pathway component in the black-legged tick"],"prefix":"10.1371","volume":"18","author":[{"given":"Canran","family":"Feng","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kyosuke","family":"Torimaru","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mandy Yu Theng","family":"Lim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Li-Ling","family":"Chak","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Masami","family":"Shiimori","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kosuke","family":"Tsuji","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tetsuya","family":"Tanaka","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Junko","family":"Iida","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8316-0960","authenticated-orcid":true,"given":"Katsutomo","family":"Okamura","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2023,3,30]]},"reference":[{"key":"pone.0281195.ref001","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1038\/nrm.2016.174","article-title":"RNA-based recognition and targeting: sowing the seeds of specificity","volume":"18","author":"SA Gorski","year":"2017","journal-title":"Nat Rev Mol Cell Biol"},{"key":"pone.0281195.ref002","doi-asserted-by":"crossref","first-page":"aad5147","DOI":"10.1126\/science.aad5147","article-title":"Diverse evolutionary roots and mechanistic variations of the CRISPR-Cas systems","volume":"353","author":"P Mohanraju","year":"2016","journal-title":"Science"},{"key":"pone.0281195.ref003","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1007\/s00294-006-0078-x","article-title":"On the origin and functions of RNA-mediated silencing: from protists to man","volume":"50","author":"H Cerutti","year":"2006","journal-title":"Curr Genet"},{"key":"pone.0281195.ref004","doi-asserted-by":"crossref","first-page":"1193","DOI":"10.1038\/nature07415","article-title":"Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals","volume":"455","author":"A Grimson","year":"2008","journal-title":"Nature"},{"key":"pone.0281195.ref005","doi-asserted-by":"crossref","first-page":"673","DOI":"10.1038\/nrm2479","article-title":"Endogenous small interfering RNAs in animals","volume":"9","author":"K Okamura","year":"2008","journal-title":"Nat Rev Mol Cell Biol"},{"key":"pone.0281195.ref006","doi-asserted-by":"crossref","first-page":"246","DOI":"10.1038\/nrm3089","article-title":"PIWI-interacting small RNAs: the vanguard of genome defence","volume":"12","author":"MC Siomi","year":"2011","journal-title":"Nat Rev Mol Cell Biol"},{"key":"pone.0281195.ref007","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1038\/s41576-018-0073-3","article-title":"PIWI-interacting RNAs: small RNAs with big functions","volume":"20","author":"DM Ozata","year":"2019","journal-title":"Nat Rev Genet"},{"key":"pone.0281195.ref008","doi-asserted-by":"crossref","first-page":"899","DOI":"10.1261\/rna.065839.118","article-title":"siRNAs and piRNAs collaborate for transposon control in the two-spotted spider mite","volume":"24","author":"M Mondal","year":"2018","journal-title":"RNA"},{"key":"pone.0281195.ref009","doi-asserted-by":"crossref","first-page":"e202000731","DOI":"10.26508\/lsa.202000731","article-title":"Exploiting somatic piRNAs in Bemisia tabac i enables novel gene silencing through RNA feeding","volume":"3","author":"M Mondal","year":"2020","journal-title":"Life Sci Alliance"},{"key":"pone.0281195.ref010","doi-asserted-by":"crossref","first-page":"e1007183","DOI":"10.1371\/journal.pgen.1007183","article-title":"Rewired RNAi-mediated genome surveillance in house dust mites","volume":"14","author":"M Mondal","year":"2018","journal-title":"PLOS Genet"},{"key":"pone.0281195.ref011","doi-asserted-by":"crossref","first-page":"174","DOI":"10.1038\/s41559-017-0403-4","article-title":"Pan-arthropod analysis reveals somatic piRNAs as an ancestral defence against transposable elements","volume":"2","author":"SH Lewis","year":"2018","journal-title":"Nat Ecol Evol"},{"key":"pone.0281195.ref012","doi-asserted-by":"crossref","first-page":"1493","DOI":"10.1534\/g3.113.006742","article-title":"The Developmental Transcriptome of the Mosquito Aedes aegypti, an Invasive Species and Major Arbovirus Vector","volume":"3","author":"OS Akbari","year":"2013","journal-title":"G3&#58; Genes|Genomes|Genetics"},{"key":"pone.0281195.ref013","doi-asserted-by":"crossref","first-page":"632","DOI":"10.1038\/nri2824","article-title":"RNA-based antiviral immunity","volume":"10","author":"SW Ding","year":"2010","journal-title":"Nat Rev Immunol"},{"key":"pone.0281195.ref014","doi-asserted-by":"crossref","first-page":"452","DOI":"10.1126\/science.1125694","article-title":"RNA Interference Directs Innate Immunity Against Viruses in Adult Drosophila","volume":"312","author":"X-HH Wang","year":"2006","journal-title":"Science"},{"key":"pone.0281195.ref015","doi-asserted-by":"crossref","first-page":"1606","DOI":"10.1073\/pnas.0911353107","article-title":"Virus discovery by deep sequencing and assembly of virus-derived small silencing RNAs","volume":"107","author":"Q Wu","year":"2010","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pone.0281195.ref016","doi-asserted-by":"crossref","first-page":"1394","DOI":"10.1038\/s41564-018-0265-9","article-title":"Immune priming and clearance of orally acquired RNA viruses in Drosophila","volume":"3","author":"JA Mondotte","year":"2018","journal-title":"Nat Microbiol"},{"key":"pone.0281195.ref017","doi-asserted-by":"crossref","first-page":"580","DOI":"10.1016\/j.cub.2006.01.065","article-title":"Natural selection drives extremely rapid evolution in antiviral RNAi genes","volume":"16","author":"DJ Obbard","year":"2006","journal-title":"Curr Biol"},{"key":"pone.0281195.ref018","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1098\/rstb.2008.0168","article-title":"The evolution of RNAi as a defence against viruses and transposable elements","volume":"364","author":"DJ Obbard","year":"2009","journal-title":"Philos Trans R Soc L B Biol Sci"},{"key":"pone.0281195.ref019","doi-asserted-by":"crossref","first-page":"537","DOI":"10.1016\/S1097-2765(02)00651-2","article-title":"Evidence that siRNAs function as guides, not primers, in the Drosophila and human RNAi pathways","volume":"10","author":"DS Schwarz","year":"2002","journal-title":"Mol Cell"},{"key":"pone.0281195.ref020","doi-asserted-by":"crossref","first-page":"465","DOI":"10.1016\/S0092-8674(01)00576-1","article-title":"On the role of RNA amplification in dsRNA-triggered gene silencing","volume":"107","author":"T Sijen","year":"2001","journal-title":"Cell"},{"key":"pone.0281195.ref021","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1016\/S0960-9822(00)00323-7","article-title":"EGO-1 is related to RNA-directed RNA polymerase and functions in germ-line development and RNA interference in C. elegans","volume":"10","author":"A Smardon","year":"2000","journal-title":"Curr Biol"},{"key":"pone.0281195.ref022","doi-asserted-by":"crossref","first-page":"10233","DOI":"10.1073\/pnas.94.19.10233","article-title":"Isolation of quelling-defective (qde) mutants impaired in posttranscriptional transgene-induced gene silencing in Neurospora crassa","volume":"94","author":"C Cogoni","year":"1997","journal-title":"Proc Natl Acad Sci"},{"key":"pone.0281195.ref023","doi-asserted-by":"crossref","first-page":"543","DOI":"10.1016\/S0092-8674(00)80864-8","article-title":"An RNA-Dependent RNA Polymerase Gene in Arabidopsis Is Required for Posttranscriptional Gene Silencing Mediated by a Transgene but Not by a Virus","volume":"101","author":"T Dalmay","year":"2000","journal-title":"Cell"},{"key":"pone.0281195.ref024","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1186\/1471-2199-10-26","article-title":"Evidence of a tick RNAi pathway by comparative genomics and reverse genetics screen of targets with known loss-of-function phenotypes","volume":"10","author":"S Kurscheid","year":"2009","journal-title":"Drosophila. BMC Mol Biol"},{"key":"pone.0281195.ref025","doi-asserted-by":"crossref","first-page":"791","DOI":"10.1186\/s12864-020-07162-0","article-title":"A genome-wide screening for RNAi pathway proteins in Acari","volume":"21","author":"BT Nganso","year":"2020","journal-title":"BMC Genomics"},{"key":"pone.0281195.ref026","doi-asserted-by":"crossref","first-page":"e1007915","DOI":"10.1371\/journal.pgen.1007915","article-title":"Functional lability of RNA-dependent RNA polymerases in animals","volume":"15","author":"N Pinz\u00f3n","year":"2019","journal-title":"PLOS Genet"},{"key":"pone.0281195.ref027","doi-asserted-by":"crossref","first-page":"351","DOI":"10.1002\/wrna.113","article-title":"Diversity of animal small RNA pathways and their biological utility","volume":"3","author":"K. Okamura","year":"2012","journal-title":"Wiley Interdiscip Rev RNA"},{"key":"pone.0281195.ref028","doi-asserted-by":"crossref","first-page":"9436","DOI":"10.1093\/nar\/gku657","article-title":"Induction and suppression of tick cell antiviral RNAi responses by tick-borne flaviviruses","volume":"42","author":"E Schnettler","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"pone.0281195.ref029","doi-asserted-by":"crossref","first-page":"1037","DOI":"10.1126\/science.1221551","article-title":"The crystal structure of human Argonaute2","volume":"336","author":"NT Schirle","year":"2012","journal-title":"Science"},{"key":"pone.0281195.ref030","doi-asserted-by":"crossref","first-page":"427","DOI":"10.1007\/s10493-015-9908-1","article-title":"An Ixodes scapularis cell line with a predominantly neuron-like phenotype","volume":"66","author":"JD Oliver","year":"2015","journal-title":"Exp Appl Acarol"},{"key":"pone.0281195.ref031","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1146\/annurev-genet-120417-031441","article-title":"piRNA-Guided Genome Defense: From Biogenesis to Silencing","volume":"52","author":"B Czech","year":"2018","journal-title":"Annu Rev Genet"},{"key":"pone.0281195.ref032","doi-asserted-by":"crossref","first-page":"652","DOI":"10.1038\/ncb1872","article-title":"Arginine methylation of Piwi proteins catalysed by dPRMT5 is required for Ago3 and Aub stability","volume":"11","author":"Y Kirino","year":"2009","journal-title":"Nat Cell Biol"},{"key":"pone.0281195.ref033","doi-asserted-by":"crossref","first-page":"3647","DOI":"10.1016\/j.celrep.2018.05.051","article-title":"Piwi Nuclear Localization and Its Regulatory Mechanism in Drosophila Ovarian Somatic Cells","volume":"23","author":"R Yashiro","year":"2018","journal-title":"Cell Rep"},{"key":"pone.0281195.ref034","doi-asserted-by":"crossref","first-page":"885","DOI":"10.1016\/j.cell.2012.10.022","article-title":"Protection from Feed-Forward Amplification in an Amplified RNAi Mechanism","volume":"151","author":"J Pak","year":"2012","journal-title":"Cell"},{"key":"pone.0281195.ref035","doi-asserted-by":"crossref","first-page":"667","DOI":"10.1093\/nar\/gkj474","article-title":"HEN1 recognizes 21\u201324 nt small RNA duplexes and deposits a methyl group onto the 2\u2019 OH of the 3\u2019 terminal nucleotide","volume":"34","author":"Z. Yang","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"pone.0281195.ref036","doi-asserted-by":"crossref","first-page":"818","DOI":"10.1038\/nature09039","article-title":"Structural basis for 5\u2019-nucleotide base-specific recognition of guide RNA by human AGO2","volume":"465","author":"F Frank","year":"2010","journal-title":"Nature"},{"key":"pone.0281195.ref037","doi-asserted-by":"crossref","first-page":"4087","DOI":"10.1021\/bi300497x","article-title":"Unique 2\u2032-O-Methylation by Hen1 in Eukaryotic RNA Interference and Bacterial RNA Repair","volume":"51","author":"RH Huang","year":"2012","journal-title":"Biochemistry"},{"key":"pone.0281195.ref038","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1016\/j.cub.2007.12.049","article-title":"Argonaute loading improves the 5\u2019 precision of both MicroRNAs and their miRNA strands in flies","volume":"18","author":"H Seitz","year":"2008","journal-title":"Curr Biol"},{"key":"pone.0281195.ref039","doi-asserted-by":"crossref","first-page":"1077","DOI":"10.1126\/science.1157396","article-title":"Endogenous siRNAs Derived from Transposons and mRNAs in Drosophila Somatic Cells","volume":"320","author":"M Ghildiyal","year":"2008","journal-title":"Science"},{"key":"pone.0281195.ref040","doi-asserted-by":"crossref","first-page":"1265","DOI":"10.1016\/j.cub.2007.06.030","article-title":"The Drosophila RNA methyltransferase, DmHen1, modifies germline piRNAs and single-stranded siRNAs in RISC","volume":"17","author":"MD Horwich","year":"2007","journal-title":"Curr Biol"},{"key":"pone.0281195.ref041","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1016\/j.ymeth.2007.09.009","article-title":"Identification of microRNAs and other small regulatory RNAs using cDNA library sequencing","volume":"44","author":"M Hafner","year":"2008","journal-title":"Methods"},{"key":"pone.0281195.ref042","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1016\/j.molcel.2009.09.020","article-title":"Distinct argonaute-mediated 22G-RNA pathways direct genome surveillance in the C. elegans germline","volume":"36","author":"W Gu","year":"2009","journal-title":"Mol Cell"},{"key":"pone.0281195.ref043","doi-asserted-by":"crossref","first-page":"105718","DOI":"10.1016\/j.actatropica.2020.105718","article-title":"miRNA profile of extracellular vesicles isolated from saliva of Haemaphysalis longicornis tick","volume":"212","author":"M Nawaz","year":"2020","journal-title":"Acta Trop"},{"key":"pone.0281195.ref044","doi-asserted-by":"crossref","first-page":"101427","DOI":"10.1016\/j.ttbdis.2020.101427","article-title":"Analysis of microRNA expression profiles dynamic in different life stages of Haemaphysalis longicornis ticks by deep sequencing of small RNA libraries","volume":"11","author":"W Liu","year":"2020","journal-title":"Ticks Tick Borne Dis"},{"key":"pone.0281195.ref045","doi-asserted-by":"crossref","first-page":"e1010119","DOI":"10.1371\/journal.ppat.1010119","article-title":"Antiviral RNA interference in disease vector (Asian longhorned) ticks","volume":"17","author":"Y Xu","year":"2021","journal-title":"PLoS Pathog"},{"key":"pone.0281195.ref046","doi-asserted-by":"crossref","first-page":"1328","DOI":"10.1016\/j.cell.2020.07.023","article-title":"Large-Scale Comparative Analyses of Tick Genomes Elucidate Their Genetic Diversity and Vector Capacities","volume":"182","author":"N Jia","year":"2020","journal-title":"Cell"},{"key":"pone.0281195.ref047","doi-asserted-by":"crossref","first-page":"779","DOI":"10.1038\/nmeth.3033","article-title":"Sets and intersections","volume":"11","author":"A Lex","year":"2014","journal-title":"Nat Methods"},{"key":"pone.0281195.ref048","doi-asserted-by":"crossref","first-page":"17036","DOI":"10.1038\/nplants.2017.36","article-title":"The poly(A) tail blocks RDR6 from converting self mRNAs into substrates for gene silencing","volume":"3","author":"K Baeg","year":"2017","journal-title":"Nat Plants"},{"key":"pone.0281195.ref049","doi-asserted-by":"crossref","first-page":"577","DOI":"10.1002\/wrna.1232","article-title":"Degradation of oligouridylated histone mRNAs: see UUUUU and goodbye","volume":"5","author":"KP Hoefig","year":"2014","journal-title":"Wiley Interdiscip Rev RNA"},{"key":"pone.0281195.ref050","doi-asserted-by":"crossref","first-page":"3154","DOI":"10.1074\/mcp.M115.051938","article-title":"Integrated Metabolomics, Transcriptomics and Proteomics Identifies Metabolic Pathways Affected by Anaplasma phagocytophilum Infection in Tick Cells*","volume":"14","author":"M Villar","year":"2015","journal-title":"Mol Cell Proteomics"},{"key":"pone.0281195.ref051","doi-asserted-by":"crossref","first-page":"9451","DOI":"10.1073\/pnas.1921046117","article-title":"RepeatModeler2 for automated genomic discovery of transposable element families","volume":"117","author":"JM Flynn","year":"2020","journal-title":"Proc Natl Acad Sci"},{"key":"pone.0281195.ref052","doi-asserted-by":"crossref","first-page":"1089","DOI":"10.1016\/j.cell.2007.01.043","article-title":"Discrete Small RNA-Generating Loci as Master Regulators of Transposon Activity in Drosophila","volume":"128","author":"J Brennecke","year":"2007","journal-title":"Cell"},{"key":"pone.0281195.ref053","doi-asserted-by":"crossref","first-page":"1587","DOI":"10.1126\/science.1140494","article-title":"A slicer-mediated mechanism for repeat-associated siRNA 5\u2019 end formation in Drosophila","volume":"315","author":"LS Gunawardane","year":"2007","journal-title":"Science"},{"key":"pone.0281195.ref054","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1186\/s13071-019-3574-9","article-title":"Characterization of an iron-inducible Haemaphysalis longicornis tick-derived promoter in an Ixodes scapularis-derived tick cell line (ISE6)","volume":"12","author":"EP Hernandez","year":"2019","journal-title":"Parasit Vectors"},{"key":"pone.0281195.ref055","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1146\/annurev-ento-033020-090410","article-title":"The Interplay Between Viruses and RNAi Pathways in Insects","volume":"66","author":"BC Bonning","year":"2021","journal-title":"Annu Rev Entomol"},{"key":"pone.0281195.ref056","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1016\/j.ttbdis.2016.10.005","article-title":"Putative RNA viral sequences detected in an Ixodes scapularis-derived cell line","volume":"8","author":"R Nakao","year":"2017","journal-title":"Ticks Tick Borne Dis"},{"key":"pone.0281195.ref057","doi-asserted-by":"crossref","first-page":"6191","DOI":"10.1093\/nar\/gkv587","article-title":"Sequence-independent characterization of viruses based on the pattern of viral small RNAs produced by the host","volume":"43","author":"ERGR Aguiar","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"pone.0281195.ref058","doi-asserted-by":"crossref","first-page":"130","DOI":"10.1016\/j.virol.2016.10.017","article-title":"VirusDetect: An automated pipeline for efficient virus discovery using deep sequencing of small RNAs","volume":"500","author":"Y Zheng","year":"2017","journal-title":"Virology"},{"key":"pone.0281195.ref059","doi-asserted-by":"crossref","first-page":"e1002061","DOI":"10.1371\/journal.pbio.1002061","article-title":"Ancient and Novel Small RNA Pathways Compensate for the Loss of piRNAs in Multiple Independent Nematode Lineages","volume":"13","author":"P Sarkies","year":"2015","journal-title":"PLOS Biol"},{"key":"pone.0281195.ref060","doi-asserted-by":"crossref","first-page":"e2019276118","DOI":"10.1073\/pnas.2019276118","article-title":"Assembly of a dsRNA synthesizing complex: RNA-DEPENDENT RNA POLYMERASE 2 contacts the largest subunit of NUCLEAR RNA POLYMERASE IV","volume":"118","author":"V Mishra","year":"2021","journal-title":"Proc Natl Acad Sci"},{"key":"pone.0281195.ref061","doi-asserted-by":"crossref","first-page":"1124","DOI":"10.1016\/j.molcel.2015.04.002","article-title":"Mechanism of Transcription Termination by RNA Polymerase III Utilizes a Non-template Strand Sequence-Specific Signal Element","volume":"58","author":"AG Arimbasseri","year":"2015","journal-title":"Mol Cell"},{"key":"pone.0281195.ref062","doi-asserted-by":"crossref","first-page":"2179","DOI":"10.15252\/embj.201694857","article-title":"TUT\u2010DIS3L2 is a mammalian surveillance pathway for aberrant structured non\u2010coding RNAs","volume":"35","author":"D Ustianenko","year":"2016","journal-title":"EMBO J"},{"key":"pone.0281195.ref063","doi-asserted-by":"crossref","first-page":"2417","DOI":"10.15252\/embj.201695164","article-title":"Molecular basis for cytoplasmic RNA surveillance by uridylation\u2010triggered decay in Drosophila","volume":"35","author":"MM Reim\u00e3o\u2010Pinto","year":"2016","journal-title":"EMBO J"},{"key":"pone.0281195.ref064","doi-asserted-by":"crossref","first-page":"gkw649","DOI":"10.1093\/nar\/gkw649","article-title":"Perlman syndrome nuclease DIS3L2 controls cytoplasmic non-coding RNAs and provides surveillance pathway for maturing snRNAs","author":"A \u0141abno","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"pone.0281195.ref065","doi-asserted-by":"crossref","first-page":"407","DOI":"10.1016\/j.cell.2015.01.010","article-title":"A Ribonuclease Coordinates siRNA Amplification and mRNA Cleavage during RNAi","volume":"160","author":"H-Y Tsai","year":"2015","journal-title":"Cell"},{"key":"pone.0281195.ref066","doi-asserted-by":"crossref","first-page":"258","DOI":"10.1038\/nsmb.3376","article-title":"RdRP-synthesized antisense ribosomal siRNAs silence pre-rRNA via the nuclear RNAi pathway","volume":"24","author":"X Zhou","year":"2017","journal-title":"Nat Struct Mol Biol"},{"key":"pone.0281195.ref067","doi-asserted-by":"crossref","first-page":"254","DOI":"10.1091\/mbc.e09-09-0790","article-title":"Centromeric Localization of Dispersed Pol III Genes in Fission Yeast. Bloom KS, editor","volume":"21","author":"O Iwasaki","year":"2010","journal-title":"Mol Biol Cell"},{"key":"pone.0281195.ref068","doi-asserted-by":"crossref","first-page":"859","DOI":"10.1016\/j.cell.2006.04.028","article-title":"A Role for TFIIIC Transcription Factor Complex in Genome Organization","volume":"125","author":"K Noma","year":"2006","journal-title":"Cell"},{"key":"pone.0281195.ref069","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1016\/j.cell.2016.02.057","article-title":"A Tunable Mechanism Determines the Duration of the Transgenerational Small RNA Inheritance in C. elegans","volume":"165","author":"L Houri-Ze\u2019evi","year":"2016","journal-title":"Cell"},{"key":"pone.0281195.ref070","doi-asserted-by":"crossref","first-page":"533","DOI":"10.1016\/S0092-8674(00)80863-6","article-title":"Arabidopsis SGS2 and SGS3 Genes Are Required for Posttranscriptional Gene Silencing and Natural Virus Resistance","volume":"101","author":"P Mourrain","year":"2000","journal-title":"Cell"},{"key":"pone.0281195.ref071","doi-asserted-by":"crossref","first-page":"15209","DOI":"10.1128\/JVI.79.24.15209-15217.2005","article-title":"RDR6 Has a Broad-Spectrum but Temperature-Dependent Antiviral Defense Role in Nicotiana benthamiana","volume":"79","author":"F Qu","year":"2005","journal-title":"J Virol"},{"key":"pone.0281195.ref072","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1016\/j.virol.2015.02.028","article-title":"viral silencing suppressors: Tools forged to fine-tune host-pathogen coexistence","volume":"479\u2013480","author":"T Csorba","year":"2015","journal-title":"Virology"},{"key":"pone.0281195.ref073","doi-asserted-by":"crossref","first-page":"15025","DOI":"10.1073\/pnas.1303193110","article-title":"ERK signaling couples nutrient status to antiviral defense in the insect gut","volume":"110","author":"J Xu","year":"2013","journal-title":"Proc Natl Acad Sci"},{"key":"pone.0281195.ref074","doi-asserted-by":"crossref","first-page":"450","DOI":"10.1016\/j.pt.2007.07.009","article-title":"Tick cell lines: tools for tick and tick-borne disease research","volume":"23","author":"L Bell-Sakyi","year":"2007","journal-title":"Trends Parasitol"},{"key":"pone.0281195.ref075","doi-asserted-by":"crossref","first-page":"219","DOI":"10.1007\/BF01194061","article-title":"Formulation of medium for tick cell culture","volume":"7","author":"UG Munderloh","year":"1989","journal-title":"Exp Appl Acarol"},{"key":"pone.0281195.ref076","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1016\/j.cell.2007.06.028","article-title":"The mirtron pathway generates microRNA-class regulatory RNAs in Drosophila","volume":"130","author":"K Okamura","year":"2007","journal-title":"Cell"},{"key":"pone.0281195.ref077","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.38389","article-title":"Importance of miRNA stability and alternative primary miRNA isoforms in gene regulation during Drosophila development","volume":"7","author":"L Zhou","year":"2018","journal-title":"Elife"},{"key":"pone.0281195.ref078","doi-asserted-by":"crossref","first-page":"297","DOI":"10.12688\/f1000research.13635.1","article-title":"A draft genome sequence for the Ixodes scapularis cell line, ISE6","volume":"7","author":"JR Miller","year":"2018","journal-title":"F1000Research"},{"key":"pone.0281195.ref079","first-page":"155","article-title":"miRBase: from microRNA sequences to function","volume":"47","author":"A Kozomara","year":"2019"},{"key":"pone.0281195.ref080","doi-asserted-by":"crossref","first-page":"D212","DOI":"10.1093\/nar\/gkaa921","article-title":"RNAcentral 2021: secondary structure integration, improved sequence search and new member databases","volume":"49","author":"BA Sweeney","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"pone.0281195.ref081","doi-asserted-by":"crossref","DOI":"10.1007\/978-1-4939-0931-5","volume-title":"Animal Endo-SiRNAs","author":"A Werner","year":"2014"},{"key":"pone.0281195.ref082","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1038\/nmeth.4285","article-title":"ModelFinder: fast model selection for accurate phylogenetic estimates","volume":"14","author":"S Kalyaanamoorthy","year":"2017","journal-title":"Nat Methods"},{"key":"pone.0281195.ref083","doi-asserted-by":"crossref","first-page":"518","DOI":"10.1093\/molbev\/msx281","article-title":"UFBoot2: Improving the Ultrafast Bootstrap Approximation","volume":"35","author":"DT Hoang","year":"2018","journal-title":"Mol Biol Evol"},{"key":"pone.0281195.ref084","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1093\/molbev\/msu300","article-title":"IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies","volume":"32","author":"L-T Nguyen","year":"2015","journal-title":"Mol Biol Evol"},{"key":"pone.0281195.ref085","article-title":"ColabFold\u2014Making protein folding accessible to all","author":"M Mirdita","year":"2021","journal-title":"bioRxiv"},{"key":"pone.0281195.ref086","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1038\/s41586-021-03819-2","article-title":"Highly accurate protein structure prediction with AlphaFold","volume":"596","author":"J Jumper","year":"2021","journal-title":"Nature"},{"key":"pone.0281195.ref087","doi-asserted-by":"crossref","first-page":"10","DOI":"10.14806\/ej.17.1.200","article-title":"Cutadapt removes adapter sequences from high-throughput sequencing reads","volume":"17","author":"M. Martin","year":"2011","journal-title":"EMBnet.journal"},{"key":"pone.0281195.ref088","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1038\/nmeth.4197","article-title":"Salmon provides fast and bias-aware quantification of transcript expression","volume":"14","author":"R Patro","year":"2017","journal-title":"Nat Methods"},{"key":"pone.0281195.ref089","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"MI Love","year":"2014","journal-title":"Genome Biol"},{"key":"pone.0281195.ref090","first-page":"100141","article-title":"clusterProfiler 4.0: A universal enrichment tool for interpreting omics data","volume":"2","author":"T Wu","year":"2021","journal-title":"Innov"},{"key":"pone.0281195.ref091","article-title":"eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale","author":"C Carlos","year":"2021","journal-title":"bioRxiv"},{"key":"pone.0281195.ref092","article-title":"TRAPID 2.0: a web application for taxonomic and functional analysis of de novo transcriptomes","author":"F Bucchini","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"pone.0281195.ref093","doi-asserted-by":"crossref","first-page":"644","DOI":"10.1038\/nbt.1883","article-title":"Full-length transcriptome assembly from RNA-Seq data without a reference genome","volume":"29","author":"MG Grabherr","year":"2011","journal-title":"Nat Biotechnol"},{"key":"pone.0281195.ref094","doi-asserted-by":"crossref","first-page":"1795","DOI":"10.1016\/j.celrep.2016.04.059","article-title":"The Drosophila Dicer-1 Partner Loquacious Enhances miRNA Processing from Hairpins with Unstable Structures at the Dicing Site","volume":"15","author":"MY Lim","year":"2016","journal-title":"Cell Rep"},{"key":"pone.0281195.ref095","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1186\/s13071-017-2011-1","article-title":"Tick-borne pathogens induce differential expression of genes promoting cell survival and host resistance in Ixodes ricinus cells","volume":"10","author":"KL Mansfield","year":"2017","journal-title":"Parasit Vectors"}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0281195","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,3,30]],"date-time":"2023-03-30T13:54:50Z","timestamp":1680184490000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0281195"}},"subtitle":[],"editor":[{"given":"S\u00e9bastien","family":"Pfeffer","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2023,3,30]]},"references-count":95,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2023,3,30]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0281195","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,3,30]]}}}